Harvester Ii

Bioinformatic Harvester II Education and Training A cademia S inica I nstitute of B io m edical S ciences Biomedical IT Core Ming-Fang Tsai [email_address]

Agenda 1. Overview 3. Introduction to Databases 4. Summary 2. Advance Search

Feature Overview ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

http://harvester.embl.de ,[object Object],[object Object],[object Object],[object Object]

Flow Diagram Text results Genome Gene position localization Domain : : Graphical results Sequence Saved as a file Human Mouse Rat Cross Link Input page rank

General Query chromosome 4q32 human chromosome 4q32 107 筆 P42262 P42262 Text results Genome Graphical results Save as a file Input

General Query chromosome 4q32 human chromosome 4q32 brain brain hypothetical Text results Genome Graphical results Save as a file Input 善用 AND 及 NOT 功能 , 可有效縮小範圍 , 原 107 筆減為 20 筆資料

Exercise ,[object Object],[object Object]

6q21-6q24, not hypothetical 可以使用自定 protein list 的功能 , 稍後將會介紹 Q: 如果想查 6q21,6q24, brain 的資料 , 要怎麼做呢 ?

如何將查詢結果另存新檔 ? ,[object Object],Text results Genome Graphical results Save as a file Input Text results 跟 graphical results 都是相同方式存檔哦 ! Graphical results

User Defined Protein List ,[object Object],[object Object],2345 第一次需設定密碼 , 以後憑此密碼調出資料 Protein set ID 回功能頁 Protein 之間以空格或換行分開 , 都可以

Protein-Set Search 2345 注意 : 密碼最好設定複雜一點 , 萬一有人輸入相同密碼 , 則一樣可以存取你的資料 .

Exercise ,[object Object],[object Object],[object Object],[object Object]

如何查詢 6q21, 6q24, brain? ,[object Object],得到 272 筆資料

如何查詢 6q21, 6q24, brain? ,[object Object]

[object Object],如何查詢 6q21, 6q24, brain? 複製欄位 B 的 protein list

Sequence Search QARENKDFVR http://www-db.embl.de/jss/servlet/de.embl.bk.htmlfind.HarvesterOutputMysql?m = seqSearch 此處可以是任意長度任意字 ,[object Object],[object Object]

Sequence Pattern Search ,[object Object],[object Object],[object Object],[object Object],[object Object]

Send sequence to STRING,BLAST,SMART, CDART ,[object Object],[object Object]

Term Search by application ,[object Object],[object Object],[object Object],[object Object],[object Object]

Sequence Search by application ,[object Object],[object Object]

Template ,[object Object],keyword url 連結方法 sequence

Practice ,[object Object],[object Object],http://www-db.embl.de/jss/servlet/de.embl.bk.htmlfind.HarvesterOutputMysql?m = seqSearch ,[object Object]

[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

http://genome-www5.stanford.edu/cgi-bin/source/sourceSearch

Source Batch Search ,[object Object]

GFP-cDNA ,[object Object],[object Object],[object Object]

GFP-cDNA ,[object Object],輸入方式跟 Harvester 一樣

SMART ,[object Object],[object Object],[object Object],[object Object],[object Object]

PSORT ,[object Object],[object Object],[object Object]

SOSUI ,[object Object],[object Object],[object Object],[object Object],[object Object]

SOSUI Result http://sosui.proteome.bio.tuat.ac.jp/cgi-bin/adv_sosui.cgi

iHOP ,[object Object],Gene defining information interaction

GoPubmed ,[object Object],[object Object]

Summary ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Harvester Ii

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